|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
39-1127 |
0e+00 |
|
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Pssm-ID: 238353 [Multi-domain] Cd Length: 866 Bit Score: 1231.28 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 39 LVKQHIDSFNYFINVEIKKIMKANEKVTSDA-DPMWYLKYLNIYVGLPDVEESfNVTRPVSPHECRLRDMTYSAPITVDI 117
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDdDGRLKLKFGDIYLGKPKVEEG-GVTRKLTPNECRLRDLTYSAPLYVDI 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 118 EYTRGSQRIIR-NALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIVEaDRK 196
Cdd:cd00653 80 RLTVNDKGKIKeQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 197 GAVGASVTSSTHEKKSRTNMAVKQGRFYLRHNTLSEDIPIviifkamgvesdqeivqmigteehvmaafgpsleecqkaq 276
Cdd:cd00653 159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 277 iftQMQALKYIGNKVrrqrmwgggpkktkieearellastilthvpvkefnfrakcIYTAVMVRRVI-LAQGDNKVDDRD 355
Cdd:cd00653 199 ---QEEALKYIGKRF-----------------------------------------EDLIYMIRKLIlLVLGKGKLDDID 234
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 356 YYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRaaQFDVVKHMRQDQITNGMVNAISTGNWSLKRFKMDRQG 435
Cdd:cd00653 235 HLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKK--DLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSG 312
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 436 VTQVLSRLSYISALGMMTRISS-QFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITtdmedgpivkl 514
Cdd:cd00653 313 LSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS----------- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 515 asnlgvedvnllcgeelsypnvflvflngnilgvirdhkklvntfrlmrragyinefvsistnltdrcvyissdgGRLCR 594
Cdd:cd00653 382 ---------------------------------------------------------------------------GRIER 386
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 595 PYIIVKKQkpavtnkhmeelaqgyrnfedflheslveyldvneendcnialyehtinkdTTHLEIEPFTLLGVCAGLIPY 674
Cdd:cd00653 387 PYRIVEKE---------------------------------------------------VTHIEISPSQILSVAASLIPF 415
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 675 PHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDA 754
Cdd:cd00653 416 PEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDA 495
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 755 LVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMldaaTRKPIWRHEILDADGICSPGEKVENKQVLVNKSMPT 834
Cdd:cd00653 496 IIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDI----PNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPK 571
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 835 VTQIPLEGSNVPQQpQYKDVPITYKGATDSYIEKVMISS---NAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIV 911
Cdd:cd00653 572 GETESTPIFGEKAR-DVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKIL 650
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 912 PQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTS 991
Cdd:cd00653 651 PQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYD 730
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 992 GITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMIS 1071
Cdd:cd00653 731 GRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIK 810
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|....*.
gi 28277230 1072 SDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLK 1127
Cdd:cd00653 811 SDDVVARVCVKCGIILSANLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
26-1129 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1078.82 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 26 KWRLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMKAnEKVTSDADPMWYLKYLNIYVGLPDVEESFNVTRPVSPHECRLR 105
Cdd:PRK08565 1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDE-FGEIKTEIPGLKIVLGKIRVGEPEIKEADGSERPITPMEARLR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 106 DMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLS 185
Cdd:PRK08565 80 NLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLA 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 186 KNRIIVEADRKGA---VGASVTSSTHEKKSRTNMA-VKQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMIGTEEHV 261
Cdd:PRK08565 160 PNRVLVDKGEAGSsitHTAKVISSRAGYRAQVTVErRKDGTIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSLDPEI 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 262 MAAFGPSLEECQKAQIfTQMQALKYIGNKVRRqrmwgGGPKKTKIEEARELLASTILTHVPVKEFNFRAKCIYTAVMVRR 341
Cdd:PRK08565 240 QQELLPSLEQASSIAA-TVEDALDYIGKRVAI-----GQPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASK 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 342 VI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVkhMRQDQITNGMVNAIS 420
Cdd:PRK08565 314 LLeLYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAI--VRPDIITERIRHALA 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 421 TGNWSlkrfkMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMT 500
Cdd:PRK08565 392 TGNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMA 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 501 HITTDMEDGPIVKLASNLGVEDVNLLCGEElsYPNVFLVFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTD 580
Cdd:PRK08565 467 QISVGVDEEEVEEILYELGVVPVEEAREEE--YISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAYIETG 544
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 581 --RCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIALYEHTINKDTTHLE 658
Cdd:PRK08565 545 eiNEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPEHTHLE 624
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 659 IEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQN 738
Cdd:PRK08565 625 IWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQN 704
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 739 ATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPG 818
Cdd:PRK08565 705 AVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPE 784
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 819 EKVENKQVLVNK-SMPTVTQIPLEGSNVPQQpqYKDVPITYKGATDSYIEKVMISSNAEDAFLIKMLLRQTRRPEIGDKF 897
Cdd:PRK08565 785 VEVKGGDVLIGKtSPPRFLEELEELSLGLQE--RRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKF 862
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 898 SSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLV 977
Cdd:PRK08565 863 ASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELL 942
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 978 RHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIG 1057
Cdd:PRK08565 943 KLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIG 1022
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 28277230 1058 YGASMLLLERLMISSDAFEVDVCGQCGLLGYSG------WCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLS 1129
Cdd:PRK08565 1023 HGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDrrknkyVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKLG 1100
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
539-1129 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Pssm-ID: 274713 [Multi-domain] Cd Length: 599 Bit Score: 699.86 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 539 VFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGY 618
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 619 RNFEDFLHESLVEYLDVNEENDCNIALYEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 698
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 699 YNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 778
Cdd:TIGR03670 161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 779 LKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLVNK-SMPTVTQIPLEGSNVPQQpqYKDVPIT 857
Cdd:TIGR03670 241 ERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKtSPPRFLEELREFGLVTER--RRDTSVT 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 858 YKGATDSYIEKVMISSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSR 937
Cdd:TIGR03670 319 VRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSR 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 938 MTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVL 1017
Cdd:TIGR03670 399 MTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVA 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 1018 DKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGY------SGW 1091
Cdd:TIGR03670 479 DKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWedkrkgTAY 558
|
570 580 590
....*....|....*....|....*....|....*...
gi 28277230 1092 CHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLS 1129
Cdd:TIGR03670 559 CPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELG 596
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
31-1129 |
0e+00 |
|
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439855 [Multi-domain] Cd Length: 1001 Bit Score: 593.24 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 31 PAFLKVKGLVKQHIDSFNYFINVEIKKIMKaNEKVTSDADPMWYLKYLNIYVGLPdveesfnvtrPVSPHECRLRDMTYS 110
Cdd:COG0085 8 KEPLELPNLLEIQLDSFNWFLEEGLQEIFD-EISPIEDFTGNLSLEFGDYRLGEP----------KYTPEECKERDLTYA 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 111 APITVDIEYT-RGSQRIIRNALPIGRMPIMLRSsncvltgktpaefaklnecpldpgGYFIVKGVEKVILIQEQLSKNRI 189
Cdd:COG0085 77 APLYVKVRLVnKETGEIKEQEVFMGDFPLMTDS------------------------GTFIINGTERVIVSQLVRSPGVY 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 190 IVEADRKGA---VGASVTSSTH-----EKKSRTNMAVKQGRfylrhntlSEDIPIVIIFKAMGVESDQEIVQMIG---TE 258
Cdd:COG0085 133 FVEEEDKSGkdlYSAKVIPSRGawlefETDKDGTIYVRIDR--------KRKIPVTVLLRALGLETDEEILEAFGddpIQ 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 259 EHVMaafgPSLEecqKAQIFTQMQALKYIGNKVRRqrmwgGGPKKtkIEEARELLASTI-------LTHV---------- 321
Cdd:COG0085 205 EYIL----ATLE---KDNTKTQEEALLEIYRKLRP-----GEPPT--IERAEQLLDNLFfdpkrydLAHVgrykinkklg 270
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 322 -PVKEFNFRAKCIYTAVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFnseMKKIADQvIPKQRAAQ 399
Cdd:COG0085 271 lDVPPEDRVLTAEDIVATIKYLLeLHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRM---ERVVRER-MTTQDVEA 346
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 400 FDVVKHMRQDQITNGMVNAISTGNwsLKRFkMDRqgvTQVLSRLSY---ISALGM--MTRISSQFEktrkVsgpRSLQPS 474
Cdd:COG0085 347 ITPQSLINIRPVVAAIKEFFGSSQ--LSQF-MDQ---TNPLSELTHkrrLSALGPggLSRERAGFE----V---RDVHPS 413
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 475 QWGMLCPSDTPEGEACGLVKNLALMthittdmedgpivklasnlgvedvnllcgeelsypnvflvflngnilgvirdhkk 554
Cdd:COG0085 414 HYGRMCPIETPEGPNIGLIGSLALY------------------------------------------------------- 438
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 555 lvntfrlmrraGYINEFvsistnltdrcvyissdgGRLCRPYIIVKKQKpaVTNKhmeelaqgyrnfedflheslVEYLD 634
Cdd:COG0085 439 -----------ARVNEY------------------GFIETPYRKVENGK--VTDE--------------------IEYLT 467
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 635 VNEENDCNIALYEHTINKDT-----------------------THLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGK 691
Cdd:COG0085 468 ADEEENYYIAQANAPLDEDGnfleervlvryrgeevlvppeevDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQR 547
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 692 QAMG-----------TIGYNQRNRIDTlmyllAYPQKPMVKT----KTIELI------EFEKLPAGQNATVAVMSYSGYD 750
Cdd:COG0085 548 QAVPllrpeapllhyPLQKFQRSNQGT-----CINQRPIVRVgdrvEKGDVLadgpatDNGELALGQNLLVAFMPWEGYN 622
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 751 IEDALVLNKASLDRGFGRCLVYKNAKCTLKRY----TNQTFDKvmgPML-DAATRKpiwrheiLDADGICSPGEKVENKQ 825
Cdd:COG0085 623 YEDAIIISERLVKDDVLTSIHIEEYEIEARDTklgpEEITRDI---PNVsEEALRN-------LDEDGIIRIGAEVKGGD 692
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 826 VLVNK-SMPTVTQIPLE-----------GSNVpqqpqyKD----VPITYKGatdsYIEKVMISSNAEDAFL-------IK 882
Cdd:COG0085 693 ILVGKvTPKGETELTPEerllraifgekAREV------RDtslrVPHGEKG----KVIDVKVFSREEGDELppgvnklVR 762
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 883 MLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGT 962
Cdd:COG0085 763 VYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATP 842
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 963 AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRD 1042
Cdd:COG0085 843 VFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQF 922
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 1043 GGLRLGEMERDCLIGYGASMLLLERLMISSDafevDVCgqcgllGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNI 1122
Cdd:COG0085 923 GGQRFGEMEVWALEAYGAAYTLQERLTIKSD----DVC------GRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGL 992
|
....*..
gi 28277230 1123 IPRLKLS 1129
Cdd:COG0085 993 DVEVLSE 999
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
668-1041 |
0e+00 |
|
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
Pssm-ID: 459854 [Multi-domain] Cd Length: 371 Bit Score: 569.47 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 668 CAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYS 747
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 748 GYDIEDALVLNKASLDRGFGRCLVYKnaKCTLKRYTNQTFDKVMGPMldaaTRKPIWRHEILDADGICSPGEKVENKQVL 827
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPIEEITRDI----PNVSEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 828 VNKSMPTVTQIPLEGSNVPQQPQYKDVPITYKGATDSYIEKVMI-SSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGV 906
Cdd:pfam00562 155 VGKVGPTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 907 CGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSK--VKDVCEDLVRHGYNYL 984
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 28277230 985 GKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSR 1041
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
539-600 |
2.59e-31 |
|
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain.
Pssm-ID: 428012 [Multi-domain] Cd Length: 62 Bit Score: 116.70 E-value: 2.59e-31
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 28277230 539 VFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVK 600
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
621-661 |
5.73e-10 |
|
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain.
Pssm-ID: 428013 [Multi-domain] Cd Length: 53 Bit Score: 55.62 E-value: 5.73e-10
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 28277230 621 FEDFLHESLVEYLDVNEENDCNIALYE-----------HTINKDT-THLEIEP 661
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPedleessreerEGPYAHTyTHCEIHP 53
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
39-1127 |
0e+00 |
|
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Pssm-ID: 238353 [Multi-domain] Cd Length: 866 Bit Score: 1231.28 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 39 LVKQHIDSFNYFINVEIKKIMKANEKVTSDA-DPMWYLKYLNIYVGLPDVEESfNVTRPVSPHECRLRDMTYSAPITVDI 117
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDdDGRLKLKFGDIYLGKPKVEEG-GVTRKLTPNECRLRDLTYSAPLYVDI 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 118 EYTRGSQRIIR-NALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIVEaDRK 196
Cdd:cd00653 80 RLTVNDKGKIKeQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 197 GAVGASVTSSTHEKKSRTNMAVKQGRFYLRHNTLSEDIPIviifkamgvesdqeivqmigteehvmaafgpsleecqkaq 276
Cdd:cd00653 159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 277 iftQMQALKYIGNKVrrqrmwgggpkktkieearellastilthvpvkefnfrakcIYTAVMVRRVI-LAQGDNKVDDRD 355
Cdd:cd00653 199 ---QEEALKYIGKRF-----------------------------------------EDLIYMIRKLIlLVLGKGKLDDID 234
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 356 YYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRaaQFDVVKHMRQDQITNGMVNAISTGNWSLKRFKMDRQG 435
Cdd:cd00653 235 HLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKK--DLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSG 312
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 436 VTQVLSRLSYISALGMMTRISS-QFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITtdmedgpivkl 514
Cdd:cd00653 313 LSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS----------- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 515 asnlgvedvnllcgeelsypnvflvflngnilgvirdhkklvntfrlmrragyinefvsistnltdrcvyissdgGRLCR 594
Cdd:cd00653 382 ---------------------------------------------------------------------------GRIER 386
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 595 PYIIVKKQkpavtnkhmeelaqgyrnfedflheslveyldvneendcnialyehtinkdTTHLEIEPFTLLGVCAGLIPY 674
Cdd:cd00653 387 PYRIVEKE---------------------------------------------------VTHIEISPSQILSVAASLIPF 415
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 675 PHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDA 754
Cdd:cd00653 416 PEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDA 495
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 755 LVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMldaaTRKPIWRHEILDADGICSPGEKVENKQVLVNKSMPT 834
Cdd:cd00653 496 IIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDI----PNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPK 571
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 835 VTQIPLEGSNVPQQpQYKDVPITYKGATDSYIEKVMISS---NAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIV 911
Cdd:cd00653 572 GETESTPIFGEKAR-DVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKIL 650
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 912 PQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTS 991
Cdd:cd00653 651 PQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYD 730
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 992 GITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMIS 1071
Cdd:cd00653 731 GRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIK 810
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|....*.
gi 28277230 1072 SDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLK 1127
Cdd:cd00653 811 SDDVVARVCVKCGIILSANLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
26-1129 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1078.82 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 26 KWRLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMKAnEKVTSDADPMWYLKYLNIYVGLPDVEESFNVTRPVSPHECRLR 105
Cdd:PRK08565 1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDE-FGEIKTEIPGLKIVLGKIRVGEPEIKEADGSERPITPMEARLR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 106 DMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLS 185
Cdd:PRK08565 80 NLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLA 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 186 KNRIIVEADRKGA---VGASVTSSTHEKKSRTNMA-VKQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMIGTEEHV 261
Cdd:PRK08565 160 PNRVLVDKGEAGSsitHTAKVISSRAGYRAQVTVErRKDGTIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSLDPEI 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 262 MAAFGPSLEECQKAQIfTQMQALKYIGNKVRRqrmwgGGPKKTKIEEARELLASTILTHVPVKEFNFRAKCIYTAVMVRR 341
Cdd:PRK08565 240 QQELLPSLEQASSIAA-TVEDALDYIGKRVAI-----GQPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASK 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 342 VI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVkhMRQDQITNGMVNAIS 420
Cdd:PRK08565 314 LLeLYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAI--VRPDIITERIRHALA 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 421 TGNWSlkrfkMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMT 500
Cdd:PRK08565 392 TGNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMA 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 501 HITTDMEDGPIVKLASNLGVEDVNLLCGEElsYPNVFLVFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTD 580
Cdd:PRK08565 467 QISVGVDEEEVEEILYELGVVPVEEAREEE--YISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAYIETG 544
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 581 --RCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIALYEHTINKDTTHLE 658
Cdd:PRK08565 545 eiNEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPEHTHLE 624
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 659 IEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQN 738
Cdd:PRK08565 625 IWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQN 704
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 739 ATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPG 818
Cdd:PRK08565 705 AVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPE 784
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 819 EKVENKQVLVNK-SMPTVTQIPLEGSNVPQQpqYKDVPITYKGATDSYIEKVMISSNAEDAFLIKMLLRQTRRPEIGDKF 897
Cdd:PRK08565 785 VEVKGGDVLIGKtSPPRFLEELEELSLGLQE--RRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKF 862
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 898 SSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLV 977
Cdd:PRK08565 863 ASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELL 942
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 978 RHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIG 1057
Cdd:PRK08565 943 KLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIG 1022
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 28277230 1058 YGASMLLLERLMISSDAFEVDVCGQCGLLGYSG------WCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLS 1129
Cdd:PRK08565 1023 HGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDrrknkyVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKLG 1100
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
539-1129 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Pssm-ID: 274713 [Multi-domain] Cd Length: 599 Bit Score: 699.86 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 539 VFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGY 618
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 619 RNFEDFLHESLVEYLDVNEENDCNIALYEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 698
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 699 YNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 778
Cdd:TIGR03670 161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 779 LKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLVNK-SMPTVTQIPLEGSNVPQQpqYKDVPIT 857
Cdd:TIGR03670 241 ERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKtSPPRFLEELREFGLVTER--RRDTSVT 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 858 YKGATDSYIEKVMISSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSR 937
Cdd:TIGR03670 319 VRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSR 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 938 MTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVL 1017
Cdd:TIGR03670 399 MTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVA 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 1018 DKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGY------SGW 1091
Cdd:TIGR03670 479 DKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWedkrkgTAY 558
|
570 580 590
....*....|....*....|....*....|....*...
gi 28277230 1092 CHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLS 1129
Cdd:TIGR03670 559 CPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELG 596
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
539-1128 |
0e+00 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 693.24 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 539 VFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGY 618
Cdd:PRK07225 7 VYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKNGE 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 619 RNFEDFLHESLVEYLDVNEENDCNIALYEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 698
Cdd:PRK07225 87 LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEEHTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPA 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 699 YNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 778
Cdd:PRK07225 167 ANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGE 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 779 LKRYTNQTFDKVMGPMLD--AATRKPIWRHeiLDADGICSPGEKVENKQVLVNK-SMPTVTQIPLEGSNVPQQpqYKDVP 855
Cdd:PRK07225 247 ERRYPGGQEDRFEIPDKDvrGYRGEEAYRH--LDEDGLVNPETEVKEGDVLIGKtSPPRFLEEPDDFGISPEK--RRETS 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 856 ITYKGATDSYIEKVMISSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFP 935
Cdd:PRK07225 323 VTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIP 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 936 SRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHM 1015
Cdd:PRK07225 403 SRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHM 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 1016 VLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGY------S 1089
Cdd:PRK07225 483 VANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIydkkrnR 562
|
570 580 590
....*....|....*....|....*....|....*....
gi 28277230 1090 GWCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKL 1128
Cdd:PRK07225 563 KYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLEL 601
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
31-1129 |
0e+00 |
|
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439855 [Multi-domain] Cd Length: 1001 Bit Score: 593.24 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 31 PAFLKVKGLVKQHIDSFNYFINVEIKKIMKaNEKVTSDADPMWYLKYLNIYVGLPdveesfnvtrPVSPHECRLRDMTYS 110
Cdd:COG0085 8 KEPLELPNLLEIQLDSFNWFLEEGLQEIFD-EISPIEDFTGNLSLEFGDYRLGEP----------KYTPEECKERDLTYA 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 111 APITVDIEYT-RGSQRIIRNALPIGRMPIMLRSsncvltgktpaefaklnecpldpgGYFIVKGVEKVILIQEQLSKNRI 189
Cdd:COG0085 77 APLYVKVRLVnKETGEIKEQEVFMGDFPLMTDS------------------------GTFIINGTERVIVSQLVRSPGVY 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 190 IVEADRKGA---VGASVTSSTH-----EKKSRTNMAVKQGRfylrhntlSEDIPIVIIFKAMGVESDQEIVQMIG---TE 258
Cdd:COG0085 133 FVEEEDKSGkdlYSAKVIPSRGawlefETDKDGTIYVRIDR--------KRKIPVTVLLRALGLETDEEILEAFGddpIQ 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 259 EHVMaafgPSLEecqKAQIFTQMQALKYIGNKVRRqrmwgGGPKKtkIEEARELLASTI-------LTHV---------- 321
Cdd:COG0085 205 EYIL----ATLE---KDNTKTQEEALLEIYRKLRP-----GEPPT--IERAEQLLDNLFfdpkrydLAHVgrykinkklg 270
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 322 -PVKEFNFRAKCIYTAVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFnseMKKIADQvIPKQRAAQ 399
Cdd:COG0085 271 lDVPPEDRVLTAEDIVATIKYLLeLHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRM---ERVVRER-MTTQDVEA 346
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 400 FDVVKHMRQDQITNGMVNAISTGNwsLKRFkMDRqgvTQVLSRLSY---ISALGM--MTRISSQFEktrkVsgpRSLQPS 474
Cdd:COG0085 347 ITPQSLINIRPVVAAIKEFFGSSQ--LSQF-MDQ---TNPLSELTHkrrLSALGPggLSRERAGFE----V---RDVHPS 413
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 475 QWGMLCPSDTPEGEACGLVKNLALMthittdmedgpivklasnlgvedvnllcgeelsypnvflvflngnilgvirdhkk 554
Cdd:COG0085 414 HYGRMCPIETPEGPNIGLIGSLALY------------------------------------------------------- 438
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 555 lvntfrlmrraGYINEFvsistnltdrcvyissdgGRLCRPYIIVKKQKpaVTNKhmeelaqgyrnfedflheslVEYLD 634
Cdd:COG0085 439 -----------ARVNEY------------------GFIETPYRKVENGK--VTDE--------------------IEYLT 467
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 635 VNEENDCNIALYEHTINKDT-----------------------THLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGK 691
Cdd:COG0085 468 ADEEENYYIAQANAPLDEDGnfleervlvryrgeevlvppeevDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQR 547
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 692 QAMG-----------TIGYNQRNRIDTlmyllAYPQKPMVKT----KTIELI------EFEKLPAGQNATVAVMSYSGYD 750
Cdd:COG0085 548 QAVPllrpeapllhyPLQKFQRSNQGT-----CINQRPIVRVgdrvEKGDVLadgpatDNGELALGQNLLVAFMPWEGYN 622
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 751 IEDALVLNKASLDRGFGRCLVYKNAKCTLKRY----TNQTFDKvmgPML-DAATRKpiwrheiLDADGICSPGEKVENKQ 825
Cdd:COG0085 623 YEDAIIISERLVKDDVLTSIHIEEYEIEARDTklgpEEITRDI---PNVsEEALRN-------LDEDGIIRIGAEVKGGD 692
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 826 VLVNK-SMPTVTQIPLE-----------GSNVpqqpqyKD----VPITYKGatdsYIEKVMISSNAEDAFL-------IK 882
Cdd:COG0085 693 ILVGKvTPKGETELTPEerllraifgekAREV------RDtslrVPHGEKG----KVIDVKVFSREEGDELppgvnklVR 762
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 883 MLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGT 962
Cdd:COG0085 763 VYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATP 842
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 963 AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRD 1042
Cdd:COG0085 843 VFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQF 922
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 1043 GGLRLGEMERDCLIGYGASMLLLERLMISSDafevDVCgqcgllGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNI 1122
Cdd:COG0085 923 GGQRFGEMEVWALEAYGAAYTLQERLTIKSD----DVC------GRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGL 992
|
....*..
gi 28277230 1123 IPRLKLS 1129
Cdd:COG0085 993 DVEVLSE 999
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
668-1041 |
0e+00 |
|
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
Pssm-ID: 459854 [Multi-domain] Cd Length: 371 Bit Score: 569.47 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 668 CAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYS 747
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 748 GYDIEDALVLNKASLDRGFGRCLVYKnaKCTLKRYTNQTFDKVMGPMldaaTRKPIWRHEILDADGICSPGEKVENKQVL 827
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPIEEITRDI----PNVSEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 828 VNKSMPTVTQIPLEGSNVPQQPQYKDVPITYKGATDSYIEKVMI-SSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGV 906
Cdd:pfam00562 155 VGKVGPTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 907 CGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSK--VKDVCEDLVRHGYNYL 984
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 28277230 985 GKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSR 1041
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
24-523 |
3.33e-114 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 363.89 E-value: 3.33e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 24 EEKWRLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMKANEKVTSDADPMWYLKYLNIYVGLPDVEESFNVTRPVSPHECR 103
Cdd:PRK09606 3 EDRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDGVYVELGKIRVGKPVVKEADGSEREIYPMEAR 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 104 LRDMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQ 183
Cdd:PRK09606 83 LRNLTYSAPLYLEMSPVEGGEEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLED 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 184 LSKNRIIVEADRKGA---VGASVTSSTH--------EKKsrtnmavKQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIV 252
Cdd:PRK09606 163 LAPNKILVEKDERYGdriEVAKVFSQRRgyralvtvERN-------RDGLLEVSFPSVPGSIPFVILMRALGLETDEEIV 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 253 QMIGTEEHVMAAFGPSLEEcqkAQIFTQMQALKYIGNKVRrqrmwGGGPKKTKIEEARELLASTILTHVPVKEFNFRAKC 332
Cdd:PRK09606 236 EAVSDDPEIVKFMLENLEE---AEVDTQEEALEYIGKRVA-----PGQTKEYRIKRAEYVIDRYLLPHLGVEPEVRRAKA 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 333 IYTAVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIADQVipKQRAAQFDVVKHMRQDQI 411
Cdd:PRK09606 308 HYLGRMAEACFeLALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERA--NMRNRELSIKTAVRSDVL 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 412 TNGMVNAISTGNWslkrfKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACG 491
Cdd:PRK09606 386 TERLEHAMATGNW-----VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCG 460
|
490 500 510
....*....|....*....|....*....|..
gi 28277230 492 LVKNLALMTHITTDMEDGPIVKLASNLGVEDV 523
Cdd:PRK09606 461 LVKNFAQMVEISTGEDEEEVKEILKELGVEPE 492
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
38-413 |
9.75e-112 |
|
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.
Pssm-ID: 367994 [Multi-domain] Cd Length: 396 Bit Score: 353.61 E-value: 9.75e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 38 GLVKQHIDSFNYFINVEIKKIMKANEKVTSDADP--------MWYLKYLNIYVGLPDVEESFNVTRPVSPHECRLRDMTY 109
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIqhpgengdKLSLKFGQIRLGKPMFDETDGSTREIYPQECRLRNLTY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 110 SAPITVDIEYTR-GSQRIIRNALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNR 188
Cdd:pfam04563 81 SAPLYVDLELSVyNGEDIKPIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQEHRSRNH 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 189 IIVEADR---KGAVGASVTSSTHE-----KKSRTNMA--VKQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMIGTE 258
Cdd:pfam04563 161 PIVFKKAdpkKRGSVASVRSSAEIsvrpdSTSWVNVLeyLSNGTIYFKFPYIKKEIPIVIILRALGFTSDREIFELICYD 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 259 EH---VMAAFGPSLEECQKAQIFTQMQALKYIGNKVR-RQRMwgGGPKKTKIEEARELLASTILTHVPVKEFNFRAKCIY 334
Cdd:pfam04563 241 VNdqqLQEELLPSLEEGFKIRIQTQEQALDYIGGRGRaIFRM--GRPREPRIKYAEEILQKEVLPHLGTYELDETKKAYF 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 335 TAVMVRRVIL-AQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRAaqFDVVKHMRQDQITN 413
Cdd:pfam04563 319 IGYMIRRLLLlALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDD--LMLQLLVNAKPITS 396
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
31-1120 |
1.96e-67 |
|
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 273928 [Multi-domain] Cd Length: 1065 Bit Score: 247.27 E-value: 1.96e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 31 PAFLKVKGLVKQHIDSFNYFINVEIKKIMKAN---EKVTSDADPM------WYLKYLNIYVGLPDVeesfnvtrpvSPHE 101
Cdd:TIGR02013 12 PEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEeglEEVFKSIFPIedytgnIELEYLSYRLGEPKY----------SVEE 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 102 CRLRDMTYSAPITVDIEYT----RGSQRIIRNALPIGRMPIMlrssncvlTGKtpaefaklnecpldpgGYFIVKGVEKV 177
Cdd:TIGR02013 82 CKERGLTYSAPLKVKLRLInkeeDGTKEIKEQDVYMGDIPLM--------TDR----------------GTFIINGAERV 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 178 ILIQEQLSKNRIIVEADRKGAVGASVTSST----------HEKKSRTNMAVKQGRfylrhntlSEDIPIVIIFKAMGVES 247
Cdd:TIGR02013 138 VVSQLHRSPGVFFSSEKDTTKSGKVLFSARiipyrgswleFETDKKDVLYVRIDR--------KRKLPATVLLRALGYTI 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 248 DQEIVQMIGTEEHVMAAFgpsleecQKAQIFTQMQALKYIGNKVRrqrmwGGGPkkTKIEEARELLASTI-------LTH 320
Cdd:TIGR02013 210 DTLILNRLGSGEYIRNTL-------RKDPTNSEEEALVEIYRKLR-----PGEP--PTVEAARSLLENLFfdpkrydLGR 275
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 321 VPVKEFNFRAK-------CIYT-----AVMVRRVILAQGDNKVDDRDYYGNKRLELAGQLLsllfEDLFKKFNSEMKKIA 388
Cdd:TIGR02013 276 VGRYKLNKKLGldvpesiGVLTkediiATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELL----QNQFRVGLARMERIV 351
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 389 dqvipKQRAAQFDVVKHMRQDQITNGMVNAIST---GNWSLKRFkMDRqgvTQVLSRLSY---ISALGM--MTRISSQFE 460
Cdd:TIGR02013 352 -----RERMSTQDTDTLTPQDLINAKPISAAIKeffGSSQLSQF-MDQ---TNPLAELTHkrrLSALGPggLTRERAGFE 422
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 461 KtrkvsgpRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITtdmEDGPIvklasnlgvedvnllcgeELSYPNVflvf 540
Cdd:TIGR02013 423 V-------RDVHPTHYGRICPIETPEGPNIGLINSLSTYARVN---EYGFI------------------ETPYRKV---- 470
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 541 lngnilgviRDHKKLVntfrlmrragyinefvsistnlTDRCVYISSDGGRlcrPYIIVKKQKPAVTNKHM-EELAQG-Y 618
Cdd:TIGR02013 471 ---------KDGKVVV----------------------TDEIDYLTADEED---NYVIAQANAPLDENGRFvEDLVVArY 516
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 619 RNFEDFLHESLVEYLDVNeendcnialyehtinkdtthleiePFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAM---- 694
Cdd:TIGR02013 517 RGEITLVSPDQVDYMDVS------------------------PKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVpllr 572
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 695 ---------------------------GTIGYNQRNRI---------DTLMYLLAYP--------------QKPMV---- 720
Cdd:TIGR02013 573 seaplvgtgmeakvardsgavivakrgGVVEYVDAKRIvirydedeeEPDGGIDIYRllkyqrsnqdtcinQRPIVsvgd 652
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 721 KTKTIELI------EFEKLPAGQNATVAVMSYSGYDIEDALVLNKasldrgfgrCLVYKNAKCT--LKRYTNQTFDKVMG 792
Cdd:TIGR02013 653 RVEAGDVLadgpstDLGELALGRNVLVAFMPWNGYNYEDAILISE---------RLVKDDVFTSihIEEYEVEARDTKLG 723
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 793 P---------MLDAATRKpiwrheiLDADGICSPGEKVENKQVLVNKSMPT-VTQIPLE-----------GSNVpqqpqy 851
Cdd:TIGR02013 724 PeeitrdipnVSEEALRN-------LDENGIVRIGAEVKAGDILVGKVTPKgETELTPEekllraifgekARDV------ 790
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 852 KDVPITYKGATDSYIEKVMISSNAEDAFL-------IKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGIC 924
Cdd:TIGR02013 791 RDTSLRVPPGVEGTVIDVKVFSREQGDELppgvnklVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTP 870
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 925 PDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRF--HYGTA-FGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAY 1001
Cdd:TIGR02013 871 VDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKgvPIATPvFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRP 950
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 1002 IYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSD-------A 1074
Cdd:TIGR02013 951 VTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDdvvgrtkA 1030
|
1210 1220 1230 1240
....*....|....*....|....*....|....*....|....*.
gi 28277230 1075 FEVDVCGQcgllgysgwchycksscHVSSLRIPYACKLLFQELQSM 1120
Cdd:TIGR02013 1031 YEAIVKGE-----------------NVPEPGIPESFNVLIKELQSL 1059
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
35-1133 |
6.32e-57 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 214.95 E-value: 6.32e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 35 KVKGLVKQHIDSFNYFINVEIKKIMKANEKVTsdaDPMWYLKYLNIYvglpdveESFNVTRP-VSPHECRLRDMTYSAPI 113
Cdd:CHL00207 6 ALPDFLEIQRTSFCWFLNEGLNEELNIFSKIF---DYTGNLELLLFG-------KNYKLKYPkYNLLSAKSYDSNYSIQI 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 114 TVDIEYTRGSQRIIRNA-LPIGRMPIMLRSSNCVLTGktpAEFAKLNECPLDPGGYFivkgvEKVILiqeqlSKNRIIVE 192
Cdd:CHL00207 76 YLPLKFINLKTNKIKFInYLIGNLPKMTQRGTFIING---LERVIVSQIIRSPGIYF-----KKEIK-----KNSNKIYS 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 193 ADRKGAVGASVTSSTHEKKsrtnmavkqgRFYLRHNTLSEdIPIVIIFKAMGVeSDQEIVQmigteeHVMAAFGPSLEEC 272
Cdd:CHL00207 143 ATLIPNRGSWIKFELDKNK----------EIWIRIDKNRK-KPLIIFLKALGL-TDQDIYS------RLTKSEFLKKLKP 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 273 QKAQI--FTQMQALKYIGNKVRRqrmwggGPKKTkIEEARELLASTILT----------------HVPVKEFNFRAKCIY 334
Cdd:CHL00207 205 ILLNSnsYTNEEILLEIYKNLSP------IEPAT-VNDANQNLFSRFFDpknydlgkvgrykinnKLNLNIPERVRNLTY 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 335 T---AVMVRRVILAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSemkkiadqVIPKQraaqfdVVKHmRQDQI 411
Cdd:CHL00207 278 EdilSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLER--------ILRNR------MTIC-DIDSL 342
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 412 TNGMVNAISTGNWSLKRFKMDRQGV-----TQVLSRLSY---ISALGmmtriSSQFEKTRKVSGPRSLQPSQWGMLCPSD 483
Cdd:CHL00207 343 SKFNLINPKPLIALIREFFGSSQLSqymdqTNPLSELTHkrrISILG-----PGGLDKDRISFAVRDIHPSHYGRICPIE 417
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 484 TPEGEACGLvknlalmthittdmedgpIVKLASNLGVEDVNLLcgeELSYPNVFlvflNGNILgvirdhKKLVNTfrlmr 563
Cdd:CHL00207 418 TPEGPNCGL------------------IGSLATNARINKFGFI---ETPFYKVI----NGKVK------KFGNPI----- 461
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 564 ragYINEFVSISTNLTdrcvyiSSDggrlcrpyIIVKKQKpAVTNKHMEELaqgYRNfedflheslvEYLDVNEENDCNI 643
Cdd:CHL00207 462 ---YLTADSEDLYRIA------PND--------INLNKNN-YFKKNIIPVR---YKQ----------EFKTVNPSKVDFI 510
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 644 AlyehtinkdtthleIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTI---------GYNQRNRIDTLM----- 709
Cdd:CHL00207 511 A--------------ISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLypekpivgtGYEKQIALDSGMtiisl 576
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 710 -------------------------YLLAYP---------QKPMV----KTKTIEL------IEFEKLPAGQNATVAVMS 745
Cdd:CHL00207 577 tegivvsvsaykiiiqddnnryihyYLQKYQrsnqntcinYRPIVwvgeKINIGQIladgsdIDNSELALGQNVLVAYMP 656
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 746 YSGYDIEDALVLNKAsldrgfgrcLVYKNAKCTLK--------RYTNQTFDKV--MGPMLDAATRKpiwrheILDADGIC 815
Cdd:CHL00207 657 WEGYNFEDAILINKR---------LVYEDLFTSIHiekyeielRQTKLGSEEItrNIPNVSEYSLK------NLDENGII 721
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 816 SPGEKVENKQVLVNKSMPTvtqiplegSNVPQQPQYK--------------DVPITYKGATDSYIEKVMI----SSNAED 877
Cdd:CHL00207 722 SIGSKVLAGDILVGKITPK--------GESDQLPEGKllraifgekakdvkDTSLRMPNGGYGRVIKVEIfsrsKGDELK 793
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 878 AFL---IKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAG-V 953
Cdd:CHL00207 794 FGYylkIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGdN 873
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 954 LDGRFH-------YGTAFggSKV---KDVCEDLVRHGYNYL------GKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVL 1017
Cdd:CHL00207 874 LNKRFKilpfdemYGSEY--SRIlinNKLNQASIKNNEYWLfnsyhpGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVD 951
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 1018 DKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafevDVCGQCGLLGYsgwchYCKS 1097
Cdd:CHL00207 952 DKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSD----DMQGRNETLNA-----IVKG 1022
|
1210 1220 1230
....*....|....*....|....*....|....*..
gi 28277230 1098 SCHVSSLrIPYACKLLFQELQSMNI-IPRLKLSKYNE 1133
Cdd:CHL00207 1023 QPIPKPG-TPESFKVLMRELQSLGLdIEAYKIENFLE 1058
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1043-1129 |
2.37e-46 |
|
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription.
Pssm-ID: 461355 [Multi-domain] Cd Length: 87 Bit Score: 160.83 E-value: 2.37e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 1043 GGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNI 1122
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAAYNKCPICKGETDISPGYIPESFKLLFQELQSLGI 80
|
....*..
gi 28277230 1123 IPRLKLS 1129
Cdd:pfam04560 81 DPRLLLE 87
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
736-1073 |
3.38e-45 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 177.79 E-value: 3.38e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 736 GQNATVAVMSYSGYDIEDALVLNKasldrgfgrCLVYKNAKCTL--KRY------TNQTFDKVMG--PMLDAAtrkpIWR 805
Cdd:CHL00001 652 GKNVLVAYMPWEGYNFEDAVLISE---------RLVYEDIYTSFhiRKYeiqthvTSQGPERITKeiPHLEAH----LLR 718
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 806 HeiLDADGICSPGEKVENKQVLVNKSMPtvtQIPLEGSNVP-----------QQPQYKD----VPITYKG-ATD-SYIEK 868
Cdd:CHL00001 719 N--LDKNGIVMLGSWVETGDILVGKLTP---QEAEESSYAPegrllraifgiQVSTSKEtclkLPIGGRGrVIDvRWIQK 793
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 869 VMISSNaeDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLA 948
Cdd:CHL00001 794 KGGSSY--NPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLL 871
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 949 GKAGVLDGRfHYG-TAFGGSKVKDVCEDLVRH---------GY------NYLGKDYVTSGITGEPLEAYIYFGPVYYQKL 1012
Cdd:CHL00001 872 GLAGDLLNR-HYRiAPFDERYEQEASRKLVFSelyeaskqtANpwvfepEYPGKSRLFDGRTGDPFEQPVTIGKAYILKL 950
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 28277230 1013 KHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSD 1073
Cdd:CHL00001 951 IHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD 1011
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
880-1081 |
3.91e-39 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 158.73 E-value: 3.91e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 880 LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRfH 959
Cdd:PRK00405 869 LVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGI-K 947
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 960 YGT-AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEG 1038
Cdd:PRK00405 948 FATpVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGG 1027
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 28277230 1039 RSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafevDVCG 1081
Cdd:PRK00405 1028 KAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD----DVVG 1066
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
539-600 |
2.59e-31 |
|
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain.
Pssm-ID: 428012 [Multi-domain] Cd Length: 62 Bit Score: 116.70 E-value: 2.59e-31
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 28277230 539 VFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVK 600
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
316-1120 |
1.20e-29 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 128.50 E-value: 1.20e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 316 TILTHVPVkefnfrakcIYTAVMVRRVILAQGdnKVDDRDYYGNKRLELAGQLLSllfEDLFKKFNSEMKKIADQVIPKQ 395
Cdd:PRK09603 430 TTLTHEDI---------ITTVKYLMKIKNNQG--KIDDRDHLGNRRIRAVGELLA---NELHSGLVKMQKTIKDKLTTMS 495
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 396 RAaqFDVVkhMRQDQITNGMVNA----ISTGNwSLKRFkMDRqgvTQVLSRLSY---ISALGmmtriSSQFEKTRKVSGP 468
Cdd:PRK09603 496 GA--FDSL--MPHDLVNSKMITStimeFFMGG-QLSQF-MDQ---TNPLSEVTHkrrLSALG-----EGGLVKDRVGFEA 561
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 469 RSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHIttdmedgpivklasnlgvedvnllcgeelsypnvflvflngNILGV 548
Cdd:PRK09603 562 RDVHPTHYGRICPIETPEGQNIGLINTLSTFTRV-----------------------------------------NDLGF 600
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 549 IR-DHKKLVNTfrlmrragyinefvsistNLTDRCVYISS---DGgrlcrpYIIVKKQKPAVTNKHMEElaqgyrnfedf 624
Cdd:PRK09603 601 IEaPYKKVVDG------------------KVVGETIYLTAiqeDS------HIIAPASTPIDEEGNILG----------- 645
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 625 lheSLVEyldvnEENDCNIALYEHTinkDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAM---------- 694
Cdd:PRK09603 646 ---DLIE-----TRVEGEIVLNEKS---KVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVpllrsdapiv 714
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 695 -------------GTIGYNQR---NRIDTL-MYLL----------AYP--------------QKPMVKT-KTIEL----- 727
Cdd:PRK09603 715 gtgiekiiardswGAIKANRAgvvEKIDSKnIYILgegkeeayidAYSlqknlrtnqntsfnQVPIVKVgDKVEAgqiia 794
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 728 ----IEFEKLPAGQNATVAVMSYSGYDIEDALVLNKasldrgfgrCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRK-P 802
Cdd:PRK09603 795 dgpsMDRGELALGKNVRVAFMPWNGYNFEDAIVVSE---------RITKDDIFTSTHIYEKEVDARELKHGVEEFTADiP 865
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 803 IWRHEI---LDADGICSPGEKVENKQVLVNKSMP-------------------------------------TVTQIPL-- 840
Cdd:PRK09603 866 DVKEEAlahLDESGIVKVGTYVSAGMILVGKTSPkgeikstpeerllraifgdkaghvvnkslycppslegTVIDVKVft 945
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 841 -------------------------------------------------------------EGSNVPQQ----------- 848
Cdd:PRK09603 946 kkgyekdarvlsayeeekakldmehfdrltmlnreellrvssllsqaileepfshngkdykEGDQIPKEeiasinrftla 1025
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 849 ---PQY-KDVPITYKGATDSYIE-KVMISSNAEDAF---------------LIKMLLRQTRRPEIGDKFSSRHGQKGVCG 908
Cdd:PRK09603 1026 slvKKYsKEVQNHYEITKNNFLEqKKVLGEEHEEKLsilekddilpngvikKVKLYIATKRKLKVGDKMAGRHGNKGIVS 1105
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 909 LIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIEL---LAGK----------------------------AGV---- 953
Cdd:PRK09603 1106 NIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMhlgLVGKefgkqiasmledktkdfakelrakmleiANAinek 1185
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 954 ----------LDGRFHYGTAFGGSK-VK---DVCEDLVRHGYNYL---------GKDYVTSGITGEPLEAYIYFGPVYYQ 1010
Cdd:PRK09603 1186 dpltihalenCSDEELLEYAKDWSKgVKmaiPVFEGISQEKFYKLfelakiamdGKMDLYDGRTGEKMRERVNVGYMYMI 1265
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 1011 KLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafevDVCGQCGllGYSG 1090
Cdd:PRK09603 1266 KLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSD----DIRGREN--AYRA 1339
|
1050 1060 1070
....*....|....*....|....*....|
gi 28277230 1091 wchyCKSSCHVSSLRIPYACKLLFQELQSM 1120
Cdd:PRK09603 1340 ----IAKGEQVGESEIPETFYVLTKELQSL 1365
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
185-363 |
2.05e-26 |
|
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).
Pssm-ID: 398318 [Multi-domain] Cd Length: 185 Bit Score: 107.43 E-value: 2.05e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 185 SKNRIIVEADRKGA-VGASVTSSTHE-KKSRTNMAVKQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMI---GTEE 259
Cdd:pfam04561 1 RSNGIYVEKELDKNgIIATYTSSLISnRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDREILDRLcydFNDP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 260 HVMAAFgpSLEECQKAQIFTQMQALKYIGNKVRrqrmwGGGPKKTKIEEARELLAST-----ILTHVPVKE--FNFRAKC 332
Cdd:pfam04561 81 QMLELL--KPELEEAENIYTQEEALDYIGKGFA-----LRRGEEPRLQRAREILYSRdpkynLNKHLGLNEpfENERLKA 153
|
170 180 190
....*....|....*....|....*....|..
gi 28277230 333 IYTAVMVRRVI-LAQGDNKVDDRDYYGNKRLE 363
Cdd:pfam04561 154 QDILYMIDRLLnLKLGRRKPDDIDHLGNKRVR 185
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
316-1073 |
3.61e-23 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 107.40 E-value: 3.61e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 316 TILTHVPVKEfnfrakciytavMVRRVILAQ-GDNKVDDRDYYGNKRLELAGQLLSllfedlfKKFNSEMKKIADQVIPK 394
Cdd:PRK14844 439 TVLTHEDIIE------------IVRKIVLLRdGQGSVDDIDHLGNRRVRSVGEFIE-------NQFRTGLLKLERAVVDS 499
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 395 QRAAQFDVVK---HMRQDQITNGMVNAISTGNwsLKRFkMDRQGVTQVLSRLSYISALGM--MTRISSQFEKtrkvsgpR 469
Cdd:PRK14844 500 MSTSSLDKVSpsdFINPKVLTNVLRDFFNSSQ--LSQF-MDQTNPLSEITHKRRLSALGPggLTRERAGFEV-------R 569
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 470 SLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITT-DMEDGPIVKLASNLGVEDVNLLCG--EELSYPNVFLVFLNGNil 546
Cdd:PRK14844 570 DVHPTHYGRICPIETPEGQNIGLINSLAIYARINKyGFIESPYRKVVNRVVTDQIEYLSAidEGLYYIADTSAKLDEN-- 647
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 547 gvirdhKKLVNTFRLMRRAGyinEFVSISTnltDRCVYISsdggrlcrpyiivkkqkpaVTNKHMEELAQgyrnfedflh 626
Cdd:PRK14844 648 ------NCFVDDMLYCRYAG---SFVMVSS---DQVSYID-------------------VSPKQVISVAA---------- 686
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 627 eSLVEYLdvnEENDCNIALYEHTINKDTTHL----------EIEPFTLLGVCA-------GLIpyphhNQSPRNTYQC-A 688
Cdd:PRK14844 687 -SLIPFL---ENDDANRALMGSNMQRQAVPLlkptaplvatGMESFVASGSGAvvlakrdGIV-----DSSDSNSIVIrA 757
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 689 MGKQAMGTIGYN-------QRNRIDTLMyllayPQKPMVKTKTI----------ELIEFEKLPAGQNATVAVMSYSGYDI 751
Cdd:PRK14844 758 FDKERVNYLDVDiyhlrkfQRSNHNTCI-----NQKPLVCVGDYvkegdviadgPAINSGELALGQNLLVAFMSWQGYNF 832
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 752 EDALVLNKASLDRGFGRCLVYKNAKCTLKrytnqtfDKVMGPmlDAATRK-PIWRHEIL---DADGICSPGEKVENKQVL 827
Cdd:PRK14844 833 EDSIIISSEVVKKDLFTSIHIEEFECVVH-------DTPLGS--EKITRAiPGVNEENLyhlDDSGIVKIGTRVGPGYIL 903
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 828 VNK-------SMPTVTQI---------------------PLEGSNVPQQ--------PQYKDVPITYKGATD-----SYI 866
Cdd:PRK14844 904 VGKvtpkpslSLPPETKLlmtifgeksfdcadsslytspDVEGTVIDVQvftrrgveENERALLIKQKEINDfekerDYI 983
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 867 ------------EKVMISSNAED--------------------------------------------------------- 877
Cdd:PRK14844 984 invtseyfydelKKLLINSGSQDrekfdsiereqwwgiglknqsiseqvkslkkdfdekvshaiaqfkrkveklhegydl 1063
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 878 ----AFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAG---- 949
Cdd:PRK14844 1064 pqgvSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwack 1143
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 950 -----------------------------------KAGVLDGR------------------------------------- 957
Cdd:PRK14844 1144 klgekvgnildeinkiksafckgirslnddnftkfAAAYLDNKkienidddeitasvlntpnknalndelnelvenylns 1223
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 958 ---------------FHYGT--------------------------------AFGGSKVKDVCEDLVRHGYNYLGKDYVT 990
Cdd:PRK14844 1224 cksaysnlrnflievYSCGSnvsicnnirdisdnnliefarklrdgipvaapVFEGPKDEQIAKLFELAGLDNSGQAVLY 1303
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28277230 991 SGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMI 1070
Cdd:PRK14844 1304 DGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTV 1383
|
...
gi 28277230 1071 SSD 1073
Cdd:PRK14844 1384 KSD 1386
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
438-501 |
2.90e-21 |
|
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site.
Pssm-ID: 428011 [Multi-domain] Cd Length: 67 Bit Score: 88.35 E-value: 2.90e-21
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 28277230 438 QVLSRLSYISALGMMTRISS---QFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTH 501
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNSprgGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
621-661 |
5.73e-10 |
|
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain.
Pssm-ID: 428013 [Multi-domain] Cd Length: 53 Bit Score: 55.62 E-value: 5.73e-10
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 28277230 621 FEDFLHESLVEYLDVNEENDCNIALYE-----------HTINKDT-THLEIEP 661
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPedleessreerEGPYAHTyTHCEIHP 53
|
|
| |
